Starting phenix.real_space_refine on Mon Jul 6 07:37:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abb_15317/07_2026/8abb_15317.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 35.287 46.186 23.863 1.00127.29 S ATOM 4207 SG CYS P 187 37.446 45.403 20.721 1.00131.48 S Time building chain proxies: 6.27, per 1000 atoms: 0.19 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.833, 128.805, 165.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.07 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 21 sheets defined 61.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 52 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.718A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.831A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.823A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.822A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 347 through 365 removed outlier: 4.039A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 382 Processing helix chain 'P' and resid 58 through 89 removed outlier: 3.587A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 100 Processing helix chain 'P' and resid 131 through 139 Processing helix chain 'P' and resid 151 through 156 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix removed outlier: 3.559A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.237A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 111 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.599A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 155 removed outlier: 4.006A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.560A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.991A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.584A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.548A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.643A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.587A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.568A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.821A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.807A pdb=" N VAL B 283 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 354 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.655A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.566A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.369A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.533A pdb=" N ILE I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'J' and resid 25 through 50 removed outlier: 3.577A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.798A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.728A pdb=" N ASN J 80 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.719A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.843A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.811A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.817A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 319 through 340 Processing helix chain 'N' and resid 347 through 365 removed outlier: 4.040A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 383 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.593A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.548A pdb=" N GLY R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 63 through 84 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.233A pdb=" N ALA Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 111 Processing helix chain 'Q' and resid 123 through 137 Processing helix chain 'Q' and resid 138 through 145 removed outlier: 3.609A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 3.994A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.561A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.996A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.588A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.670A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 414 Processing helix chain 'L' and resid 419 through 429 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.660A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.577A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.559A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.824A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.799A pdb=" N VAL M 283 " --> pdb=" O GLN M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.902A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.552A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 removed outlier: 3.918A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 321 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 31 through 34 Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.367A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.529A pdb=" N ILE T 53 " --> pdb=" O GLN T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'U' and resid 25 through 50 removed outlier: 3.616A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.801A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.727A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.903A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 176 through 177 removed outlier: 3.572A pdb=" N ARG P 202 " --> pdb=" O HIS P 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.485A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.924A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.593A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 26 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.595A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'J' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.495A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 306 through 308 removed outlier: 3.954A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.575A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.603A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1889 hydrogen bonds defined for protein. 5334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13594 1.41 - 1.61: 19564 1.61 - 1.82: 167 1.82 - 2.03: 22 2.03 - 2.23: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" N TYR S 9 " pdb=" CA TYR S 9 " ideal model delta sigma weight residual 1.458 1.622 -0.164 1.90e-02 2.77e+03 7.41e+01 bond pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 1.458 1.615 -0.157 1.90e-02 2.77e+03 6.83e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.604 -0.146 1.90e-02 2.77e+03 5.93e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.603 -0.145 1.90e-02 2.77e+03 5.82e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.467 -0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 43169 3.58 - 7.16: 1926 7.16 - 10.74: 211 10.74 - 14.32: 41 14.32 - 17.90: 5 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.89 12.44 1.14e+00 7.69e-01 1.19e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.75 12.58 1.20e+00 6.94e-01 1.10e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.14 97.06 14.08 1.56e+00 4.11e-01 8.15e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 94.47 17.53 2.20e+00 2.07e-01 6.35e+01 angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 94.48 17.52 2.20e+00 2.07e-01 6.34e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 18491 32.11 - 64.22: 934 64.22 - 96.34: 88 96.34 - 128.45: 1 128.45 - 160.56: 1 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -105.35 -17.25 0 2.50e+00 1.60e-01 4.76e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -5.62 65.62 2 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -3.99 63.99 2 1.00e+01 1.00e-02 3.88e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4561 0.190 - 0.379: 379 0.379 - 0.569: 18 0.569 - 0.759: 0 0.759 - 0.949: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.63 -0.95 2.00e-01 2.50e+01 2.25e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.63 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.67 -0.91 2.00e-01 2.50e+01 2.07e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.018 2.00e-02 2.50e+03 3.23e-02 2.34e+01 pdb=" C2A HEC D 401 " -0.025 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.026 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.047 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.039 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.022 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.059 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC O 401 " -0.013 2.00e-02 2.50e+03 3.04e-02 2.08e+01 pdb=" C1B HEC O 401 " -0.010 2.00e-02 2.50e+03 pdb=" C2B HEC O 401 " -0.014 2.00e-02 2.50e+03 pdb=" C3B HEC O 401 " -0.033 2.00e-02 2.50e+03 pdb=" C4B HEC O 401 " -0.009 2.00e-02 2.50e+03 pdb=" CAB HEC O 401 " 0.059 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " -0.006 2.00e-02 2.50e+03 pdb=" CMB HEC O 401 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEC O 401 " 0.020 2.00e-02 2.50e+03 2.98e-02 2.00e+01 pdb=" C2A HEC O 401 " 0.017 2.00e-02 2.50e+03 pdb=" C3A HEC O 401 " 0.012 2.00e-02 2.50e+03 pdb=" C4A HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CAA HEC O 401 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEC O 401 " -0.021 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " -0.056 2.00e-02 2.50e+03 pdb=" CMA HEC O 401 " 0.006 2.00e-02 2.50e+03 pdb=" NA HEC O 401 " 0.006 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 9 2.28 - 2.94: 13957 2.94 - 3.59: 48635 3.59 - 4.25: 85980 4.25 - 4.90: 136885 Nonbonded interactions: 285466 Sorted by model distance: nonbonded pdb=" O CYS P 189 " pdb=" CE MET D 235 " model vdw 1.629 3.460 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.053 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.064 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.100 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.144 3.080 ... (remaining 285461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 1 through 503) selection = (chain 'N' and resid 1 through 503) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 9 through 93 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 33.520 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.216 33382 Z= 0.659 Angle : 1.783 23.663 45365 Z= 1.114 Chirality : 0.112 0.949 4962 Planarity : 0.007 0.094 5700 Dihedral : 17.802 160.561 12014 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 3.76 % Allowed : 8.03 % Favored : 88.21 % Cbeta Deviations : 1.23 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.12), residues: 3955 helix: -1.20 (0.09), residues: 2144 sheet: -0.15 (0.25), residues: 358 loop : -0.66 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG G 76 TYR 0.051 0.007 TYR D 120 PHE 0.054 0.007 PHE C 234 TRP 0.044 0.008 TRP L 474 HIS 0.023 0.005 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01090 / 0.66 (33367) covalent geometry : angle 1.77787 / 1.11 (45352) SS BOND : bond 0.02946 / 1.65 ( 5) SS BOND : angle 2.45520 / 1.27 ( 10) hydrogen bonds : bond 0.18756 / 12.49 ( 1889) hydrogen bonds : angle 7.13307 / 5.14 ( 5334) metal coordination : bond 0.08025 / 4.01 ( 4) metal coordination : angle 17.20099 / 9.22 ( 3) Misc. bond : bond 0.12646 / 6.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 454 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9435 (tttt) cc_final: 0.9162 (ttpt) REVERT: P 92 SER cc_start: 0.9635 (t) cc_final: 0.9351 (m) REVERT: G 9 LYS cc_start: 0.9065 (mttp) cc_final: 0.8727 (ttpt) REVERT: G 50 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8843 (pm20) REVERT: G 97 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8666 (mt-10) REVERT: G 99 ASP cc_start: 0.8843 (p0) cc_final: 0.8550 (p0) REVERT: G 123 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8883 (tm-30) REVERT: F 84 GLU cc_start: 0.9230 (tt0) cc_final: 0.9017 (pt0) REVERT: F 96 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8599 (t70) REVERT: A 87 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: A 141 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8943 (tp30) REVERT: A 397 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 251 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9167 (pm20) REVERT: D 303 MET cc_start: 0.9280 (mtp) cc_final: 0.9045 (mtt) REVERT: H 51 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8179 (mtm-85) REVERT: I 30 ASP cc_start: 0.9498 (t70) cc_final: 0.8923 (t0) REVERT: J 10 LYS cc_start: 0.9610 (tttm) cc_final: 0.9350 (tptp) REVERT: J 11 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8772 (pttm) REVERT: J 55 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8542 (tpp80) REVERT: J 59 ASP cc_start: 0.9541 (m-30) cc_final: 0.9293 (m-30) REVERT: J 73 ARG cc_start: 0.8917 (ptt-90) cc_final: 0.8681 (mtm180) REVERT: J 80 ASN cc_start: 0.9214 (t0) cc_final: 0.8967 (t0) REVERT: N 197 HIS cc_start: 0.9439 (OUTLIER) cc_final: 0.8747 (p-80) REVERT: N 287 ASP cc_start: 0.8435 (t0) cc_final: 0.8045 (t0) REVERT: N 345 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8932 (mt-10) REVERT: N 369 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8762 (mtt) REVERT: E 53 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8764 (mtmt) REVERT: E 55 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8312 (p0) REVERT: E 68 MET cc_start: 0.9389 (mmm) cc_final: 0.9037 (mmm) REVERT: R 50 GLU cc_start: 0.9065 (pt0) cc_final: 0.8710 (pm20) REVERT: R 55 MET cc_start: 0.9482 (mmm) cc_final: 0.9257 (tpp) REVERT: R 117 ASP cc_start: 0.8994 (m-30) cc_final: 0.8683 (t0) REVERT: Q 114 TYR cc_start: 0.8495 (t80) cc_final: 0.8149 (t80) REVERT: Q 115 ASP cc_start: 0.9037 (p0) cc_final: 0.8475 (p0) REVERT: Q 116 HIS cc_start: 0.8828 (m-70) cc_final: 0.8327 (m-70) REVERT: Q 126 GLU cc_start: 0.9479 (mp0) cc_final: 0.8791 (mp0) REVERT: Q 133 CYS cc_start: 0.8936 (t) cc_final: 0.8674 (t) REVERT: Q 140 ASP cc_start: 0.9334 (m-30) cc_final: 0.8831 (t0) REVERT: L 87 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8167 (mtt90) REVERT: M 16 SER cc_start: 0.9541 (OUTLIER) cc_final: 0.9092 (p) REVERT: M 31 GLN cc_start: 0.9065 (mt0) cc_final: 0.8626 (tt0) REVERT: M 309 ASP cc_start: 0.9419 (m-30) cc_final: 0.9053 (t0) REVERT: M 341 TYR cc_start: 0.9202 (t80) cc_final: 0.8930 (t80) REVERT: S 78 GLU cc_start: 0.9349 (tt0) cc_final: 0.9109 (pp20) REVERT: T 30 ASP cc_start: 0.9498 (t70) cc_final: 0.9230 (t0) REVERT: T 43 ARG cc_start: 0.9238 (mtm110) cc_final: 0.8714 (ttp80) REVERT: U 55 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8592 (tpp80) REVERT: U 58 GLN cc_start: 0.9381 (tp40) cc_final: 0.9019 (mt0) REVERT: U 59 ASP cc_start: 0.9567 (m-30) cc_final: 0.9244 (m-30) REVERT: U 73 ARG cc_start: 0.8863 (ptt-90) cc_final: 0.8624 (ptt180) REVERT: U 80 ASN cc_start: 0.9209 (t0) cc_final: 0.8984 (t0) outliers start: 125 outliers final: 14 residues processed: 538 average time/residue: 0.2256 time to fit residues: 185.7495 Evaluate side-chains 356 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 329 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 215 GLN Chi-restraints excluded: chain M residue 261 SER Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 173 ASN C 202 HIS C 332 ASN P 85 GLN P 90 ASN P 115 ASN P 157 GLN G 54 ASN F 96 HIS F 109 GLN A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN D 143 HIS N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS L 317 GLN L 332 ASN L 371 ASN M 87 HIS M 197 ASN M 215 GLN M 377 ASN O 93 HIS O 143 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.051698 restraints weight = 75658.800| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 2.36 r_work: 0.2511 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2369 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.472 33382 Z= 0.136 Angle : 0.622 17.551 45365 Z= 0.307 Chirality : 0.042 0.236 4962 Planarity : 0.004 0.041 5700 Dihedral : 11.921 129.441 4881 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.20 % Allowed : 9.95 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 3955 helix: 1.02 (0.11), residues: 2150 sheet: 0.31 (0.26), residues: 366 loop : 0.07 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 54 TYR 0.018 0.002 TYR D 237 PHE 0.020 0.002 PHE L 334 TRP 0.027 0.002 TRP C 156 HIS 0.010 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (33367) covalent geometry : angle 0.61962 / 0.31 (45352) SS BOND : bond 0.00286 / 0.18 ( 5) SS BOND : angle 0.62267 / 0.32 ( 10) hydrogen bonds : bond 0.04674 / 3.09 ( 1889) hydrogen bonds : angle 4.89651 / 3.50 ( 5334) metal coordination : bond 0.01571 / 0.78 ( 4) metal coordination : angle 7.13777 / 3.85 ( 3) Misc. bond : bond 0.30442 / 18.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 357 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9035 (tttt) cc_final: 0.8781 (ttpp) REVERT: P 92 SER cc_start: 0.9421 (t) cc_final: 0.9120 (m) REVERT: G 9 LYS cc_start: 0.8776 (mttp) cc_final: 0.8448 (tttm) REVERT: G 33 LYS cc_start: 0.9301 (tttt) cc_final: 0.8943 (ttpp) REVERT: G 97 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8406 (mt-10) REVERT: G 99 ASP cc_start: 0.8655 (p0) cc_final: 0.8378 (p0) REVERT: G 123 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: F 122 ASP cc_start: 0.8308 (p0) cc_final: 0.8046 (p0) REVERT: A 397 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8044 (mt) REVERT: D 163 ASP cc_start: 0.9072 (m-30) cc_final: 0.8660 (p0) REVERT: I 7 PHE cc_start: 0.8511 (t80) cc_final: 0.8258 (m-80) REVERT: I 51 LYS cc_start: 0.9463 (ptpp) cc_final: 0.9244 (ptpp) REVERT: J 13 SER cc_start: 0.9370 (t) cc_final: 0.8945 (p) REVERT: J 55 ARG cc_start: 0.8664 (ttm-80) cc_final: 0.8084 (tpp80) REVERT: J 59 ASP cc_start: 0.9155 (m-30) cc_final: 0.8785 (m-30) REVERT: J 73 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8334 (ptp-170) REVERT: J 80 ASN cc_start: 0.9067 (t0) cc_final: 0.8733 (t0) REVERT: N 16 TYR cc_start: 0.9121 (m-80) cc_final: 0.8867 (m-80) REVERT: N 369 MET cc_start: 0.8473 (mmm) cc_final: 0.8258 (mmt) REVERT: E 53 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8513 (mtmt) REVERT: E 55 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7745 (p0) REVERT: E 68 MET cc_start: 0.8998 (mmm) cc_final: 0.8783 (mmm) REVERT: R 6 SER cc_start: 0.8962 (m) cc_final: 0.8696 (p) REVERT: R 50 GLU cc_start: 0.8336 (pt0) cc_final: 0.8136 (pm20) REVERT: Q 113 ASP cc_start: 0.8583 (t0) cc_final: 0.8286 (t0) REVERT: Q 114 TYR cc_start: 0.8510 (t80) cc_final: 0.8127 (t80) REVERT: Q 115 ASP cc_start: 0.8634 (p0) cc_final: 0.7763 (p0) REVERT: Q 116 HIS cc_start: 0.8416 (m-70) cc_final: 0.7871 (m-70) REVERT: Q 126 GLU cc_start: 0.9237 (mp0) cc_final: 0.8929 (mp0) REVERT: Q 140 ASP cc_start: 0.8797 (m-30) cc_final: 0.8424 (t0) REVERT: M 31 GLN cc_start: 0.8927 (mt0) cc_final: 0.8636 (tt0) REVERT: M 60 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.9126 (t80) REVERT: M 205 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8524 (tm-30) REVERT: M 232 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8421 (mt-10) REVERT: M 309 ASP cc_start: 0.8633 (m-30) cc_final: 0.8407 (t0) REVERT: M 373 ILE cc_start: 0.9347 (mm) cc_final: 0.9042 (tt) REVERT: S 78 GLU cc_start: 0.9093 (tt0) cc_final: 0.8791 (pp20) REVERT: S 93 LEU cc_start: 0.8635 (mt) cc_final: 0.8411 (mt) REVERT: T 30 ASP cc_start: 0.9094 (t70) cc_final: 0.8701 (t0) REVERT: T 43 ARG cc_start: 0.8878 (mtm110) cc_final: 0.8439 (ttp80) REVERT: U 51 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8245 (tm-30) REVERT: U 58 GLN cc_start: 0.8869 (tp40) cc_final: 0.8645 (mt0) REVERT: U 59 ASP cc_start: 0.9151 (m-30) cc_final: 0.8836 (m-30) REVERT: U 73 ARG cc_start: 0.8852 (ptt-90) cc_final: 0.8598 (ptt-90) REVERT: U 80 ASN cc_start: 0.9171 (t0) cc_final: 0.8850 (t0) outliers start: 40 outliers final: 12 residues processed: 385 average time/residue: 0.2025 time to fit residues: 124.4831 Evaluate side-chains 332 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 10.0000 chunk 317 optimal weight: 0.7980 chunk 252 optimal weight: 0.9980 chunk 255 optimal weight: 0.0670 chunk 160 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 292 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN P 150 GLN G 84 HIS F 109 GLN A 317 GLN B 121 GLN B 316 GLN D 93 HIS Q 131 GLN L 177 ASN M 316 GLN M 377 ASN O 93 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.051143 restraints weight = 76063.658| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 2.36 r_work: 0.2502 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9229 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.398 33382 Z= 0.141 Angle : 0.550 15.684 45365 Z= 0.268 Chirality : 0.041 0.144 4962 Planarity : 0.004 0.051 5700 Dihedral : 10.627 107.693 4833 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.17 % Allowed : 10.74 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.14), residues: 3955 helix: 1.65 (0.11), residues: 2160 sheet: 0.54 (0.26), residues: 369 loop : 0.44 (0.18), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 54 TYR 0.020 0.001 TYR A 106 PHE 0.017 0.001 PHE L 334 TRP 0.016 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (33367) covalent geometry : angle 0.54848 / 0.27 (45352) SS BOND : bond 0.00609 / 0.31 ( 5) SS BOND : angle 1.43768 / 0.67 ( 10) hydrogen bonds : bond 0.04187 / 2.76 ( 1889) hydrogen bonds : angle 4.52905 / 3.23 ( 5334) metal coordination : bond 0.01140 / 0.57 ( 4) metal coordination : angle 4.47639 / 2.42 ( 3) Misc. bond : bond 0.28799 / 16.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9023 (tttt) cc_final: 0.8711 (ttpt) REVERT: P 92 SER cc_start: 0.9441 (t) cc_final: 0.9174 (m) REVERT: P 116 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8054 (m) REVERT: G 12 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: G 33 LYS cc_start: 0.9314 (tttt) cc_final: 0.8960 (tttp) REVERT: G 97 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8427 (mt-10) REVERT: G 99 ASP cc_start: 0.8755 (p0) cc_final: 0.8494 (p0) REVERT: G 123 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8321 (tm-30) REVERT: F 93 ASP cc_start: 0.9133 (p0) cc_final: 0.8797 (p0) REVERT: F 122 ASP cc_start: 0.8415 (p0) cc_final: 0.8214 (p0) REVERT: A 397 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8014 (mt) REVERT: B 58 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: B 85 TYR cc_start: 0.9345 (m-80) cc_final: 0.9123 (m-80) REVERT: D 89 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8610 (mt-10) REVERT: I 54 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8519 (ttp-170) REVERT: J 10 LYS cc_start: 0.9319 (tptp) cc_final: 0.9005 (tptp) REVERT: J 13 SER cc_start: 0.9382 (t) cc_final: 0.8938 (p) REVERT: J 55 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8319 (tpp80) REVERT: J 73 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8209 (mtt90) REVERT: J 80 ASN cc_start: 0.9110 (t0) cc_final: 0.8742 (t0) REVERT: N 22 GLN cc_start: 0.9438 (mm-40) cc_final: 0.9112 (mm-40) REVERT: N 159 GLU cc_start: 0.8018 (pm20) cc_final: 0.7733 (pm20) REVERT: N 160 ASP cc_start: 0.8846 (m-30) cc_final: 0.8459 (m-30) REVERT: N 221 MET cc_start: 0.9480 (tpt) cc_final: 0.9159 (tpp) REVERT: N 369 MET cc_start: 0.8482 (mmm) cc_final: 0.8219 (mmt) REVERT: E 53 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8554 (mtmt) REVERT: E 55 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7741 (p0) REVERT: E 68 MET cc_start: 0.8982 (mmm) cc_final: 0.8747 (mmm) REVERT: R 50 GLU cc_start: 0.8390 (pt0) cc_final: 0.8182 (pm20) REVERT: Q 113 ASP cc_start: 0.8538 (t0) cc_final: 0.8296 (t0) REVERT: Q 114 TYR cc_start: 0.8512 (t80) cc_final: 0.8156 (t80) REVERT: Q 115 ASP cc_start: 0.8637 (p0) cc_final: 0.7719 (p0) REVERT: Q 116 HIS cc_start: 0.8432 (m-70) cc_final: 0.7922 (m90) REVERT: Q 126 GLU cc_start: 0.9190 (mp0) cc_final: 0.8932 (mp0) REVERT: Q 140 ASP cc_start: 0.8796 (m-30) cc_final: 0.8451 (t0) REVERT: L 390 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8791 (mtmm) REVERT: L 461 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8320 (p0) REVERT: M 31 GLN cc_start: 0.8965 (mt0) cc_final: 0.8670 (tt0) REVERT: M 60 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.9048 (t80) REVERT: M 170 TYR cc_start: 0.8151 (p90) cc_final: 0.7652 (p90) REVERT: M 309 ASP cc_start: 0.8716 (m-30) cc_final: 0.8491 (t0) REVERT: M 373 ILE cc_start: 0.9360 (mm) cc_final: 0.9080 (tt) REVERT: O 201 SER cc_start: 0.9460 (m) cc_final: 0.9238 (p) REVERT: O 248 MET cc_start: 0.8854 (ttp) cc_final: 0.8415 (ttp) REVERT: S 51 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8161 (ptm160) REVERT: S 78 GLU cc_start: 0.9090 (tt0) cc_final: 0.8767 (pp20) REVERT: T 30 ASP cc_start: 0.9107 (t70) cc_final: 0.8749 (t0) REVERT: T 43 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8359 (ttt180) REVERT: U 51 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8145 (tm-30) REVERT: U 55 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8309 (tpp80) REVERT: U 59 ASP cc_start: 0.9140 (m-30) cc_final: 0.8683 (m-30) REVERT: U 73 ARG cc_start: 0.8881 (ptt-90) cc_final: 0.8345 (ptt180) REVERT: U 80 ASN cc_start: 0.9229 (t0) cc_final: 0.9029 (t0) outliers start: 39 outliers final: 14 residues processed: 364 average time/residue: 0.1900 time to fit residues: 111.0855 Evaluate side-chains 340 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 316 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 220 optimal weight: 0.5980 chunk 384 optimal weight: 1.9990 chunk 337 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN F 109 GLN B 92 HIS D 93 HIS N 177 GLN Q 131 GLN M 377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.065784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.050591 restraints weight = 75985.600| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.32 r_work: 0.2489 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2351 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9248 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.387 33382 Z= 0.161 Angle : 0.549 16.447 45365 Z= 0.262 Chirality : 0.041 0.142 4962 Planarity : 0.004 0.052 5700 Dihedral : 10.099 91.812 4830 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.26 % Allowed : 11.31 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3955 helix: 1.89 (0.11), residues: 2161 sheet: 0.61 (0.27), residues: 369 loop : 0.57 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 201 TYR 0.017 0.001 TYR N 225 PHE 0.016 0.001 PHE L 334 TRP 0.016 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (33367) covalent geometry : angle 0.54657 / 0.26 (45352) SS BOND : bond 0.00310 / 0.17 ( 5) SS BOND : angle 1.51353 / 0.74 ( 10) hydrogen bonds : bond 0.03996 / 2.63 ( 1889) hydrogen bonds : angle 4.40300 / 3.14 ( 5334) metal coordination : bond 0.00689 / 0.35 ( 4) metal coordination : angle 6.06081 / 3.29 ( 3) Misc. bond : bond 0.26702 / 15.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9036 (tttt) cc_final: 0.8755 (ttpt) REVERT: C 369 MET cc_start: 0.8292 (mmt) cc_final: 0.8033 (mtt) REVERT: P 150 GLN cc_start: 0.8945 (mt0) cc_final: 0.8382 (mt0) REVERT: G 12 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: G 33 LYS cc_start: 0.9295 (tttt) cc_final: 0.8924 (tttp) REVERT: G 97 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8453 (mt-10) REVERT: G 120 ASP cc_start: 0.8915 (m-30) cc_final: 0.8682 (m-30) REVERT: G 123 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8311 (tm-30) REVERT: F 88 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8174 (mt-10) REVERT: F 122 ASP cc_start: 0.8522 (p0) cc_final: 0.8281 (p0) REVERT: A 397 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8133 (mt) REVERT: A 461 ASP cc_start: 0.8639 (p0) cc_final: 0.8403 (p0) REVERT: D 235 MET cc_start: 0.8523 (mmt) cc_final: 0.7955 (mmt) REVERT: H 88 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8859 (mp0) REVERT: I 54 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8756 (ttp80) REVERT: J 13 SER cc_start: 0.9409 (t) cc_final: 0.8891 (p) REVERT: J 55 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8449 (tpp80) REVERT: J 73 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8142 (mtt90) REVERT: J 80 ASN cc_start: 0.9120 (t0) cc_final: 0.8751 (t0) REVERT: N 287 ASP cc_start: 0.8158 (t0) cc_final: 0.7765 (t0) REVERT: N 369 MET cc_start: 0.8516 (mmm) cc_final: 0.8241 (mmt) REVERT: E 53 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8566 (mtmt) REVERT: E 55 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7703 (p0) REVERT: E 68 MET cc_start: 0.8957 (mmm) cc_final: 0.8719 (mmm) REVERT: Q 114 TYR cc_start: 0.8518 (t80) cc_final: 0.8168 (t80) REVERT: Q 115 ASP cc_start: 0.8619 (p0) cc_final: 0.7767 (p0) REVERT: Q 116 HIS cc_start: 0.8366 (m-70) cc_final: 0.7938 (m90) REVERT: Q 125 GLU cc_start: 0.8909 (mp0) cc_final: 0.8688 (mp0) REVERT: Q 126 GLU cc_start: 0.9151 (mp0) cc_final: 0.8897 (mp0) REVERT: Q 140 ASP cc_start: 0.8854 (m-30) cc_final: 0.8502 (t0) REVERT: L 390 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8799 (mtmm) REVERT: L 461 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8238 (p0) REVERT: M 31 GLN cc_start: 0.8972 (mt0) cc_final: 0.8683 (tt0) REVERT: M 60 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9062 (t80) REVERT: M 292 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8822 (p) REVERT: M 309 ASP cc_start: 0.8703 (m-30) cc_final: 0.8436 (t0) REVERT: M 373 ILE cc_start: 0.9369 (mm) cc_final: 0.9089 (tt) REVERT: O 85 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8319 (mtm) REVERT: O 193 GLN cc_start: 0.9239 (mp10) cc_final: 0.8866 (mp10) REVERT: O 201 SER cc_start: 0.9453 (m) cc_final: 0.9219 (p) REVERT: S 78 GLU cc_start: 0.9094 (tt0) cc_final: 0.8799 (pp20) REVERT: T 30 ASP cc_start: 0.9086 (t70) cc_final: 0.8734 (t0) REVERT: T 43 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8377 (ttt180) REVERT: U 51 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8459 (tm-30) REVERT: U 55 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8047 (tpp80) REVERT: U 59 ASP cc_start: 0.9113 (m-30) cc_final: 0.8670 (m-30) REVERT: U 80 ASN cc_start: 0.9270 (t0) cc_final: 0.9034 (t0) outliers start: 42 outliers final: 22 residues processed: 359 average time/residue: 0.1960 time to fit residues: 113.0094 Evaluate side-chains 339 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 1.9990 chunk 167 optimal weight: 0.1980 chunk 287 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 294 optimal weight: 0.1980 chunk 369 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 96 HIS F 109 GLN D 90 HIS Q 131 GLN L 102 HIS M 92 HIS M 121 GLN M 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.067752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.052925 restraints weight = 75206.786| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.31 r_work: 0.2544 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.357 33382 Z= 0.100 Angle : 0.497 13.369 45365 Z= 0.239 Chirality : 0.039 0.138 4962 Planarity : 0.004 0.050 5700 Dihedral : 9.539 86.667 4826 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.02 % Allowed : 11.58 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.14), residues: 3955 helix: 2.09 (0.11), residues: 2159 sheet: 0.73 (0.27), residues: 369 loop : 0.71 (0.18), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 144 TYR 0.016 0.001 TYR F 114 PHE 0.014 0.001 PHE L 334 TRP 0.012 0.001 TRP C 142 HIS 0.004 0.000 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (33367) covalent geometry : angle 0.49467 / 0.24 (45352) SS BOND : bond 0.00310 / 0.16 ( 5) SS BOND : angle 1.09999 / 0.48 ( 10) hydrogen bonds : bond 0.03571 / 2.35 ( 1889) hydrogen bonds : angle 4.26304 / 3.03 ( 5334) metal coordination : bond 0.00790 / 0.39 ( 4) metal coordination : angle 5.08135 / 2.71 ( 3) Misc. bond : bond 0.25557 / 13.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 335 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9013 (tttt) cc_final: 0.8774 (ttpp) REVERT: P 71 SER cc_start: 0.9064 (m) cc_final: 0.8829 (m) REVERT: P 150 GLN cc_start: 0.8868 (mt0) cc_final: 0.8515 (mt0) REVERT: G 12 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: G 33 LYS cc_start: 0.9280 (tttt) cc_final: 0.8921 (tttp) REVERT: G 97 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8445 (mt-10) REVERT: G 123 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8275 (tm-30) REVERT: F 88 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8163 (mt-10) REVERT: F 93 ASP cc_start: 0.9275 (p0) cc_final: 0.9017 (p0) REVERT: F 122 ASP cc_start: 0.8531 (p0) cc_final: 0.8273 (p0) REVERT: B 58 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: D 89 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8725 (mt-10) REVERT: I 42 ASP cc_start: 0.8940 (m-30) cc_final: 0.8434 (m-30) REVERT: I 51 LYS cc_start: 0.9490 (ptpp) cc_final: 0.9128 (pttm) REVERT: I 54 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8797 (ttp80) REVERT: J 13 SER cc_start: 0.9364 (t) cc_final: 0.9073 (t) REVERT: J 55 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8429 (tpp80) REVERT: J 73 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8284 (mtt90) REVERT: J 80 ASN cc_start: 0.9096 (t0) cc_final: 0.8719 (t0) REVERT: N 159 GLU cc_start: 0.8078 (pm20) cc_final: 0.7765 (pm20) REVERT: N 160 ASP cc_start: 0.8939 (m-30) cc_final: 0.8643 (m-30) REVERT: N 287 ASP cc_start: 0.8091 (t0) cc_final: 0.7688 (t0) REVERT: N 369 MET cc_start: 0.8505 (mmm) cc_final: 0.8236 (mmt) REVERT: E 53 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8471 (mtmt) REVERT: E 55 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7587 (p0) REVERT: Q 113 ASP cc_start: 0.8477 (t0) cc_final: 0.8216 (t0) REVERT: Q 114 TYR cc_start: 0.8416 (t80) cc_final: 0.8091 (t80) REVERT: Q 115 ASP cc_start: 0.8640 (p0) cc_final: 0.7878 (p0) REVERT: Q 116 HIS cc_start: 0.8338 (m-70) cc_final: 0.7853 (m-70) REVERT: Q 126 GLU cc_start: 0.9109 (mp0) cc_final: 0.8881 (mp0) REVERT: Q 140 ASP cc_start: 0.8809 (m-30) cc_final: 0.8466 (t0) REVERT: M 31 GLN cc_start: 0.8997 (mt0) cc_final: 0.8659 (tt0) REVERT: M 60 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.9010 (t80) REVERT: M 170 TYR cc_start: 0.8259 (p90) cc_final: 0.7737 (p90) REVERT: M 309 ASP cc_start: 0.8716 (m-30) cc_final: 0.8409 (t0) REVERT: M 373 ILE cc_start: 0.9368 (mm) cc_final: 0.9090 (tt) REVERT: S 78 GLU cc_start: 0.9071 (tt0) cc_final: 0.8759 (pp20) REVERT: T 30 ASP cc_start: 0.9049 (t70) cc_final: 0.8685 (t0) REVERT: T 43 ARG cc_start: 0.8688 (mtm110) cc_final: 0.8319 (ttt180) REVERT: U 51 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8512 (tm-30) REVERT: U 55 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8157 (tpp80) REVERT: U 59 ASP cc_start: 0.9086 (m-30) cc_final: 0.8660 (m-30) REVERT: U 80 ASN cc_start: 0.9243 (t0) cc_final: 0.8993 (t0) outliers start: 34 outliers final: 17 residues processed: 359 average time/residue: 0.1952 time to fit residues: 112.3105 Evaluate side-chains 332 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 310 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 352 optimal weight: 0.0030 chunk 153 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 289 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN D 90 HIS N 11 ASN Q 131 GLN M 197 ASN M 377 ASN U 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.052107 restraints weight = 75504.604| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.30 r_work: 0.2525 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9220 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.343 33382 Z= 0.122 Angle : 0.508 14.451 45365 Z= 0.242 Chirality : 0.040 0.226 4962 Planarity : 0.004 0.050 5700 Dihedral : 9.328 86.355 4824 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.99 % Allowed : 11.79 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.14), residues: 3955 helix: 2.14 (0.11), residues: 2164 sheet: 0.79 (0.27), residues: 369 loop : 0.75 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 144 TYR 0.019 0.001 TYR F 114 PHE 0.019 0.001 PHE E 64 TRP 0.013 0.001 TRP C 142 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (33367) covalent geometry : angle 0.50534 / 0.24 (45352) SS BOND : bond 0.00541 / 0.27 ( 5) SS BOND : angle 1.90960 / 0.93 ( 10) hydrogen bonds : bond 0.03650 / 2.39 ( 1889) hydrogen bonds : angle 4.22395 / 3.01 ( 5334) metal coordination : bond 0.00323 / 0.16 ( 4) metal coordination : angle 5.20182 / 2.80 ( 3) Misc. bond : bond 0.23964 / 13.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9023 (tttt) cc_final: 0.8792 (ttpp) REVERT: P 71 SER cc_start: 0.9051 (m) cc_final: 0.8815 (m) REVERT: P 150 GLN cc_start: 0.8926 (mt0) cc_final: 0.8560 (mt0) REVERT: G 12 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: G 33 LYS cc_start: 0.9291 (tttt) cc_final: 0.8921 (tttp) REVERT: G 97 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8461 (mt-10) REVERT: G 123 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8311 (tm-30) REVERT: F 88 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8121 (mt-10) REVERT: F 103 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8521 (tp30) REVERT: F 122 ASP cc_start: 0.8566 (p0) cc_final: 0.8301 (p0) REVERT: B 58 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8631 (tt0) REVERT: D 89 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8674 (mt-10) REVERT: I 42 ASP cc_start: 0.8951 (m-30) cc_final: 0.8526 (m-30) REVERT: I 51 LYS cc_start: 0.9496 (ptpp) cc_final: 0.9183 (pttt) REVERT: I 54 ARG cc_start: 0.9073 (ttp80) cc_final: 0.8818 (ttp80) REVERT: J 13 SER cc_start: 0.9406 (t) cc_final: 0.9128 (t) REVERT: J 55 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8444 (tpp80) REVERT: J 69 GLU cc_start: 0.7952 (pp20) cc_final: 0.7708 (pp20) REVERT: J 73 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8295 (mtt90) REVERT: J 80 ASN cc_start: 0.9100 (t0) cc_final: 0.8712 (t0) REVERT: N 159 GLU cc_start: 0.8080 (pm20) cc_final: 0.7851 (pm20) REVERT: N 160 ASP cc_start: 0.8962 (m-30) cc_final: 0.8711 (m-30) REVERT: N 287 ASP cc_start: 0.8114 (t0) cc_final: 0.7715 (t0) REVERT: N 369 MET cc_start: 0.8514 (mmm) cc_final: 0.8252 (mmt) REVERT: E 53 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8488 (mtmt) REVERT: E 55 ASP cc_start: 0.8252 (m-30) cc_final: 0.7587 (p0) REVERT: E 68 MET cc_start: 0.8944 (tpp) cc_final: 0.8483 (mpp) REVERT: Q 113 ASP cc_start: 0.8352 (t0) cc_final: 0.7999 (t0) REVERT: Q 114 TYR cc_start: 0.8465 (t80) cc_final: 0.8127 (t80) REVERT: Q 115 ASP cc_start: 0.8627 (p0) cc_final: 0.7860 (p0) REVERT: Q 116 HIS cc_start: 0.8340 (m-70) cc_final: 0.7886 (m-70) REVERT: Q 126 GLU cc_start: 0.9110 (mp0) cc_final: 0.8896 (mp0) REVERT: Q 140 ASP cc_start: 0.8846 (m-30) cc_final: 0.8507 (t0) REVERT: M 31 GLN cc_start: 0.9010 (mt0) cc_final: 0.8675 (tt0) REVERT: M 60 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8986 (t80) REVERT: M 292 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8850 (p) REVERT: M 309 ASP cc_start: 0.8728 (m-30) cc_final: 0.8384 (t0) REVERT: M 373 ILE cc_start: 0.9365 (mm) cc_final: 0.9087 (tt) REVERT: O 85 MET cc_start: 0.8469 (ptp) cc_final: 0.8074 (ptt) REVERT: O 193 GLN cc_start: 0.9199 (mp10) cc_final: 0.8876 (mp10) REVERT: S 78 GLU cc_start: 0.9071 (tt0) cc_final: 0.8772 (pp20) REVERT: T 30 ASP cc_start: 0.9050 (t70) cc_final: 0.8709 (t0) REVERT: T 43 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8316 (ttt180) REVERT: U 51 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8572 (tm-30) REVERT: U 55 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8135 (tpp80) REVERT: U 59 ASP cc_start: 0.9069 (m-30) cc_final: 0.8638 (m-30) REVERT: U 80 ASN cc_start: 0.9245 (t0) cc_final: 0.8996 (t0) outliers start: 33 outliers final: 20 residues processed: 340 average time/residue: 0.1897 time to fit residues: 104.5186 Evaluate side-chains 331 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 306 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 8.9990 chunk 183 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN P 115 ASN F 109 GLN D 90 HIS Q 131 GLN M 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.051112 restraints weight = 76122.009| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 2.30 r_work: 0.2502 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9239 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 33382 Z= 0.154 Angle : 0.532 16.141 45365 Z= 0.252 Chirality : 0.041 0.154 4962 Planarity : 0.004 0.050 5700 Dihedral : 9.192 85.625 4822 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.17 % Allowed : 12.09 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.14), residues: 3955 helix: 2.18 (0.11), residues: 2166 sheet: 0.83 (0.27), residues: 369 loop : 0.78 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 144 TYR 0.023 0.001 TYR G 31 PHE 0.015 0.001 PHE L 334 TRP 0.015 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (33367) covalent geometry : angle 0.52883 / 0.25 (45352) SS BOND : bond 0.00224 / 0.13 ( 5) SS BOND : angle 1.65084 / 0.82 ( 10) hydrogen bonds : bond 0.03791 / 2.48 ( 1889) hydrogen bonds : angle 4.24201 / 3.02 ( 5334) metal coordination : bond 0.00682 / 0.35 ( 4) metal coordination : angle 6.35720 / 3.45 ( 3) Misc. bond : bond 0.25185 / 14.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 316 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9023 (tttt) cc_final: 0.8793 (ttpp) REVERT: P 150 GLN cc_start: 0.8995 (mt0) cc_final: 0.8627 (mt0) REVERT: G 12 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: G 33 LYS cc_start: 0.9303 (tttt) cc_final: 0.8945 (tttp) REVERT: G 97 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8467 (mt-10) REVERT: G 123 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8290 (tm-30) REVERT: F 88 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8110 (mt-10) REVERT: F 103 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8249 (tp30) REVERT: F 122 ASP cc_start: 0.8581 (p0) cc_final: 0.8313 (p0) REVERT: B 58 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: D 89 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8655 (mt-10) REVERT: I 42 ASP cc_start: 0.8976 (m-30) cc_final: 0.8661 (m-30) REVERT: I 51 LYS cc_start: 0.9488 (ptpp) cc_final: 0.9178 (pttt) REVERT: J 13 SER cc_start: 0.9428 (t) cc_final: 0.9160 (t) REVERT: J 55 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8484 (tpp80) REVERT: J 73 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8310 (mtt90) REVERT: J 80 ASN cc_start: 0.9101 (t0) cc_final: 0.8703 (t0) REVERT: N 287 ASP cc_start: 0.8120 (t0) cc_final: 0.7726 (t0) REVERT: N 369 MET cc_start: 0.8528 (mmm) cc_final: 0.8237 (mmt) REVERT: E 53 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8422 (mtpt) REVERT: E 55 ASP cc_start: 0.8305 (m-30) cc_final: 0.7739 (p0) REVERT: E 68 MET cc_start: 0.8966 (tpp) cc_final: 0.8590 (mpp) REVERT: Q 113 ASP cc_start: 0.8297 (t0) cc_final: 0.7984 (t0) REVERT: Q 114 TYR cc_start: 0.8472 (t80) cc_final: 0.8013 (t80) REVERT: Q 115 ASP cc_start: 0.8637 (p0) cc_final: 0.7939 (p0) REVERT: Q 116 HIS cc_start: 0.8358 (m-70) cc_final: 0.7924 (m-70) REVERT: Q 126 GLU cc_start: 0.9086 (mp0) cc_final: 0.8861 (mp0) REVERT: Q 140 ASP cc_start: 0.8889 (m-30) cc_final: 0.8545 (t0) REVERT: L 390 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8821 (mtmm) REVERT: M 31 GLN cc_start: 0.9006 (mt0) cc_final: 0.8689 (tt0) REVERT: M 60 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8964 (t80) REVERT: M 292 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8857 (p) REVERT: M 309 ASP cc_start: 0.8727 (m-30) cc_final: 0.8400 (t0) REVERT: M 373 ILE cc_start: 0.9366 (mm) cc_final: 0.9080 (tt) REVERT: O 85 MET cc_start: 0.8621 (ptp) cc_final: 0.8258 (ptt) REVERT: S 78 GLU cc_start: 0.9066 (tt0) cc_final: 0.8758 (pp20) REVERT: T 30 ASP cc_start: 0.9080 (t70) cc_final: 0.8691 (t0) REVERT: T 43 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8287 (ttt180) REVERT: U 51 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8691 (tm-30) REVERT: U 55 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8116 (tpp80) REVERT: U 59 ASP cc_start: 0.9066 (m-30) cc_final: 0.8603 (m-30) REVERT: U 80 ASN cc_start: 0.9261 (t0) cc_final: 0.9006 (t0) outliers start: 39 outliers final: 23 residues processed: 344 average time/residue: 0.1852 time to fit residues: 102.6039 Evaluate side-chains 337 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 389 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 chunk 341 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 294 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN F 109 GLN D 90 HIS N 22 GLN M 377 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.066273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.051361 restraints weight = 76039.500| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.32 r_work: 0.2508 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9233 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.352 33382 Z= 0.138 Angle : 0.524 15.082 45365 Z= 0.248 Chirality : 0.040 0.139 4962 Planarity : 0.004 0.050 5700 Dihedral : 9.040 84.271 4822 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.17 % Allowed : 12.09 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.14), residues: 3955 helix: 2.21 (0.11), residues: 2164 sheet: 0.83 (0.27), residues: 369 loop : 0.79 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 54 TYR 0.021 0.001 TYR O 309 PHE 0.015 0.001 PHE L 334 TRP 0.014 0.001 TRP C 142 HIS 0.011 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (33367) covalent geometry : angle 0.52055 / 0.25 (45352) SS BOND : bond 0.00180 / 0.11 ( 5) SS BOND : angle 1.21720 / 0.61 ( 10) hydrogen bonds : bond 0.03726 / 2.44 ( 1889) hydrogen bonds : angle 4.21742 / 3.00 ( 5334) metal coordination : bond 0.00345 / 0.17 ( 4) metal coordination : angle 6.91779 / 3.70 ( 3) Misc. bond : bond 0.24047 / 14.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9030 (tttt) cc_final: 0.8798 (ttpp) REVERT: P 150 GLN cc_start: 0.8993 (mt0) cc_final: 0.8627 (mt0) REVERT: G 12 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: G 33 LYS cc_start: 0.9310 (tttt) cc_final: 0.8953 (tttp) REVERT: G 97 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8472 (mt-10) REVERT: G 123 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8291 (tm-30) REVERT: F 88 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8152 (mt-10) REVERT: F 95 LYS cc_start: 0.8964 (tptp) cc_final: 0.8750 (tptm) REVERT: F 103 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8337 (tp30) REVERT: F 122 ASP cc_start: 0.8602 (p0) cc_final: 0.8339 (p0) REVERT: B 58 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: D 89 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8644 (mt-10) REVERT: D 235 MET cc_start: 0.8807 (mmm) cc_final: 0.8572 (mmm) REVERT: I 42 ASP cc_start: 0.8989 (m-30) cc_final: 0.8569 (m-30) REVERT: I 51 LYS cc_start: 0.9471 (ptpp) cc_final: 0.9128 (pttt) REVERT: I 54 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8714 (ttp-110) REVERT: J 13 SER cc_start: 0.9432 (t) cc_final: 0.9165 (t) REVERT: J 55 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.8407 (tpp80) REVERT: J 73 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8314 (mtt90) REVERT: J 80 ASN cc_start: 0.9119 (t0) cc_final: 0.8720 (t0) REVERT: N 159 GLU cc_start: 0.8092 (pm20) cc_final: 0.7767 (pm20) REVERT: N 160 ASP cc_start: 0.8932 (m-30) cc_final: 0.8675 (m-30) REVERT: N 221 MET cc_start: 0.9454 (tpp) cc_final: 0.9240 (tpt) REVERT: N 287 ASP cc_start: 0.8124 (t0) cc_final: 0.7720 (t0) REVERT: N 369 MET cc_start: 0.8536 (mmm) cc_final: 0.8242 (mmt) REVERT: E 53 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8426 (mtpt) REVERT: E 54 LYS cc_start: 0.8987 (tppt) cc_final: 0.8726 (tmtm) REVERT: E 55 ASP cc_start: 0.8330 (m-30) cc_final: 0.7828 (p0) REVERT: E 68 MET cc_start: 0.8962 (tpp) cc_final: 0.8574 (mpp) REVERT: R 50 GLU cc_start: 0.8601 (pm20) cc_final: 0.8069 (pm20) REVERT: R 117 ASP cc_start: 0.8572 (t0) cc_final: 0.8273 (t0) REVERT: Q 113 ASP cc_start: 0.8266 (t0) cc_final: 0.7936 (t0) REVERT: Q 114 TYR cc_start: 0.8491 (t80) cc_final: 0.8033 (t80) REVERT: Q 115 ASP cc_start: 0.8643 (p0) cc_final: 0.7957 (p0) REVERT: Q 116 HIS cc_start: 0.8307 (m-70) cc_final: 0.7888 (m-70) REVERT: Q 126 GLU cc_start: 0.9081 (mp0) cc_final: 0.8872 (mp0) REVERT: Q 131 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8284 (mp10) REVERT: Q 140 ASP cc_start: 0.8907 (m-30) cc_final: 0.8550 (t0) REVERT: L 390 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8783 (mtmm) REVERT: M 31 GLN cc_start: 0.8997 (mt0) cc_final: 0.8687 (tt0) REVERT: M 60 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.9010 (t80) REVERT: M 292 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8849 (p) REVERT: M 309 ASP cc_start: 0.8733 (m-30) cc_final: 0.8414 (t0) REVERT: O 85 MET cc_start: 0.8592 (ptp) cc_final: 0.8278 (ptt) REVERT: S 78 GLU cc_start: 0.9049 (tt0) cc_final: 0.8751 (pp20) REVERT: T 30 ASP cc_start: 0.9071 (t70) cc_final: 0.8692 (t0) REVERT: T 43 ARG cc_start: 0.8669 (mtm110) cc_final: 0.8260 (ttt180) REVERT: U 51 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8714 (tm-30) REVERT: U 55 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8116 (tpp80) REVERT: U 59 ASP cc_start: 0.9058 (m-30) cc_final: 0.8589 (m-30) REVERT: U 80 ASN cc_start: 0.9257 (t0) cc_final: 0.8997 (t0) outliers start: 39 outliers final: 26 residues processed: 343 average time/residue: 0.1894 time to fit residues: 105.0812 Evaluate side-chains 342 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 0.9980 chunk 274 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 362 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 250 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN D 90 HIS M 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.066798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.051860 restraints weight = 75528.930| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.32 r_work: 0.2522 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9225 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.352 33382 Z= 0.121 Angle : 0.518 14.532 45365 Z= 0.246 Chirality : 0.040 0.138 4962 Planarity : 0.003 0.050 5700 Dihedral : 8.878 84.769 4822 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.05 % Allowed : 12.27 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.14), residues: 3955 helix: 2.25 (0.11), residues: 2162 sheet: 0.85 (0.27), residues: 369 loop : 0.82 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 54 TYR 0.019 0.001 TYR O 309 PHE 0.015 0.001 PHE L 334 TRP 0.013 0.001 TRP C 142 HIS 0.013 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (33367) covalent geometry : angle 0.51487 / 0.25 (45352) SS BOND : bond 0.00358 / 0.20 ( 5) SS BOND : angle 1.14401 / 0.58 ( 10) hydrogen bonds : bond 0.03625 / 2.38 ( 1889) hydrogen bonds : angle 4.17953 / 2.97 ( 5334) metal coordination : bond 0.00258 / 0.13 ( 4) metal coordination : angle 6.63531 / 3.58 ( 3) Misc. bond : bond 0.24351 / 13.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9008 (tttt) cc_final: 0.8773 (ttpp) REVERT: P 150 GLN cc_start: 0.9009 (mt0) cc_final: 0.8634 (mt0) REVERT: G 12 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: G 33 LYS cc_start: 0.9307 (tttt) cc_final: 0.8955 (ttpp) REVERT: G 97 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8477 (mt-10) REVERT: G 123 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 88 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8142 (mt-10) REVERT: F 95 LYS cc_start: 0.8960 (tptp) cc_final: 0.8748 (tptm) REVERT: F 103 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8308 (tp30) REVERT: F 122 ASP cc_start: 0.8606 (p0) cc_final: 0.8340 (p0) REVERT: B 58 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: D 85 MET cc_start: 0.8790 (ttm) cc_final: 0.8555 (ttp) REVERT: D 89 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8666 (mt-10) REVERT: D 235 MET cc_start: 0.8763 (mmm) cc_final: 0.8503 (mmt) REVERT: I 42 ASP cc_start: 0.8981 (m-30) cc_final: 0.8555 (m-30) REVERT: I 51 LYS cc_start: 0.9475 (ptpp) cc_final: 0.9148 (pttt) REVERT: I 54 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8627 (ttp-170) REVERT: J 13 SER cc_start: 0.9427 (t) cc_final: 0.9162 (t) REVERT: J 55 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8423 (tpp80) REVERT: J 73 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8291 (mtt90) REVERT: J 80 ASN cc_start: 0.9132 (t0) cc_final: 0.8721 (t0) REVERT: N 159 GLU cc_start: 0.8120 (pm20) cc_final: 0.7872 (pm20) REVERT: N 160 ASP cc_start: 0.8935 (m-30) cc_final: 0.8731 (m-30) REVERT: N 287 ASP cc_start: 0.8117 (t0) cc_final: 0.7726 (t0) REVERT: N 369 MET cc_start: 0.8508 (mmm) cc_final: 0.8226 (mmt) REVERT: E 53 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8425 (mtpt) REVERT: E 54 LYS cc_start: 0.8994 (tppt) cc_final: 0.8698 (tmtm) REVERT: E 55 ASP cc_start: 0.8328 (m-30) cc_final: 0.7882 (p0) REVERT: E 68 MET cc_start: 0.8951 (tpp) cc_final: 0.8603 (mpp) REVERT: R 50 GLU cc_start: 0.8660 (pm20) cc_final: 0.8418 (pm20) REVERT: R 117 ASP cc_start: 0.8569 (t0) cc_final: 0.8269 (t0) REVERT: Q 113 ASP cc_start: 0.8303 (t0) cc_final: 0.7964 (t0) REVERT: Q 114 TYR cc_start: 0.8523 (t80) cc_final: 0.8091 (t80) REVERT: Q 115 ASP cc_start: 0.8642 (p0) cc_final: 0.7964 (p0) REVERT: Q 116 HIS cc_start: 0.8331 (m-70) cc_final: 0.7911 (m-70) REVERT: Q 140 ASP cc_start: 0.8891 (m-30) cc_final: 0.8546 (t0) REVERT: L 390 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8808 (mtmm) REVERT: M 31 GLN cc_start: 0.9017 (mt0) cc_final: 0.8701 (tt0) REVERT: M 60 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8974 (t80) REVERT: M 170 TYR cc_start: 0.8336 (p90) cc_final: 0.7768 (p90) REVERT: M 292 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8857 (p) REVERT: M 309 ASP cc_start: 0.8730 (m-30) cc_final: 0.8396 (t0) REVERT: O 85 MET cc_start: 0.8564 (ptp) cc_final: 0.8271 (ptt) REVERT: O 193 GLN cc_start: 0.9244 (mp10) cc_final: 0.9021 (mp10) REVERT: S 78 GLU cc_start: 0.9044 (tt0) cc_final: 0.8731 (pp20) REVERT: T 30 ASP cc_start: 0.9063 (t70) cc_final: 0.8688 (t0) REVERT: T 43 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8272 (ttt180) REVERT: U 55 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8107 (tpp80) REVERT: U 59 ASP cc_start: 0.9054 (m-30) cc_final: 0.8583 (m-30) REVERT: U 80 ASN cc_start: 0.9246 (t0) cc_final: 0.8986 (t0) outliers start: 35 outliers final: 24 residues processed: 336 average time/residue: 0.1901 time to fit residues: 103.5276 Evaluate side-chains 336 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 306 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN D 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.067970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.052655 restraints weight = 75201.418| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.41 r_work: 0.2541 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.313 33382 Z= 0.108 Angle : 0.512 13.584 45365 Z= 0.244 Chirality : 0.039 0.138 4962 Planarity : 0.004 0.050 5700 Dihedral : 8.711 86.134 4822 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.87 % Allowed : 12.48 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.14), residues: 3955 helix: 2.28 (0.11), residues: 2163 sheet: 0.86 (0.27), residues: 369 loop : 0.86 (0.18), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 54 TYR 0.025 0.001 TYR O 309 PHE 0.014 0.001 PHE A 334 TRP 0.012 0.001 TRP C 142 HIS 0.013 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (33367) covalent geometry : angle 0.50921 / 0.24 (45352) SS BOND : bond 0.00152 / 0.10 ( 5) SS BOND : angle 1.12212 / 0.57 ( 10) hydrogen bonds : bond 0.03514 / 2.30 ( 1889) hydrogen bonds : angle 4.13833 / 2.94 ( 5334) metal coordination : bond 0.00373 / 0.18 ( 4) metal coordination : angle 6.25415 / 3.38 ( 3) Misc. bond : bond 0.22858 / 13.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 316 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8992 (tttt) cc_final: 0.8764 (ttpp) REVERT: P 150 GLN cc_start: 0.9007 (mt0) cc_final: 0.8619 (mt0) REVERT: G 12 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: G 33 LYS cc_start: 0.9300 (tttt) cc_final: 0.8912 (ttpp) REVERT: G 97 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8457 (mt-10) REVERT: G 123 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8318 (tm-30) REVERT: F 88 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8140 (mt-10) REVERT: F 95 LYS cc_start: 0.8907 (tptp) cc_final: 0.8703 (tptm) REVERT: F 103 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8400 (tp30) REVERT: F 112 GLU cc_start: 0.8771 (tp30) cc_final: 0.8408 (tp30) REVERT: F 122 ASP cc_start: 0.8581 (p0) cc_final: 0.8305 (p0) REVERT: B 58 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: D 89 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8637 (mt-10) REVERT: D 163 ASP cc_start: 0.9041 (m-30) cc_final: 0.8640 (p0) REVERT: D 235 MET cc_start: 0.8694 (mmm) cc_final: 0.8434 (mmt) REVERT: I 42 ASP cc_start: 0.8970 (m-30) cc_final: 0.8575 (m-30) REVERT: I 51 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9142 (pttt) REVERT: I 54 ARG cc_start: 0.9093 (ttp80) cc_final: 0.8620 (ttp-170) REVERT: J 13 SER cc_start: 0.9430 (t) cc_final: 0.9158 (t) REVERT: J 55 ARG cc_start: 0.8750 (ttm-80) cc_final: 0.8352 (tpp80) REVERT: J 73 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8283 (mtt90) REVERT: J 80 ASN cc_start: 0.9119 (t0) cc_final: 0.8697 (t0) REVERT: N 159 GLU cc_start: 0.8178 (pm20) cc_final: 0.7936 (pm20) REVERT: N 160 ASP cc_start: 0.8937 (m-30) cc_final: 0.8670 (m-30) REVERT: N 287 ASP cc_start: 0.8090 (t0) cc_final: 0.7670 (t0) REVERT: N 369 MET cc_start: 0.8471 (mmm) cc_final: 0.8234 (mmt) REVERT: E 53 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8365 (mtpt) REVERT: E 54 LYS cc_start: 0.9001 (tppt) cc_final: 0.8679 (tmtm) REVERT: E 55 ASP cc_start: 0.8340 (m-30) cc_final: 0.7872 (p0) REVERT: E 68 MET cc_start: 0.8898 (tpp) cc_final: 0.8554 (mpp) REVERT: R 117 ASP cc_start: 0.8500 (t0) cc_final: 0.8198 (t0) REVERT: Q 113 ASP cc_start: 0.8250 (t0) cc_final: 0.7882 (t0) REVERT: Q 114 TYR cc_start: 0.8529 (t80) cc_final: 0.8094 (t80) REVERT: Q 115 ASP cc_start: 0.8663 (p0) cc_final: 0.7993 (p0) REVERT: Q 116 HIS cc_start: 0.8321 (m-70) cc_final: 0.7906 (m-70) REVERT: Q 126 GLU cc_start: 0.9094 (mp0) cc_final: 0.8684 (mp0) REVERT: Q 131 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8216 (mp10) REVERT: Q 140 ASP cc_start: 0.8904 (m-30) cc_final: 0.8471 (t0) REVERT: M 31 GLN cc_start: 0.9007 (mt0) cc_final: 0.8675 (tt0) REVERT: M 60 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8939 (t80) REVERT: M 170 TYR cc_start: 0.8339 (p90) cc_final: 0.7773 (p90) REVERT: M 292 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8848 (p) REVERT: M 309 ASP cc_start: 0.8741 (m-30) cc_final: 0.8397 (t0) REVERT: O 85 MET cc_start: 0.8562 (ptp) cc_final: 0.8295 (ptt) REVERT: S 78 GLU cc_start: 0.9047 (tt0) cc_final: 0.8708 (pp20) REVERT: T 30 ASP cc_start: 0.9038 (t70) cc_final: 0.8667 (t0) REVERT: T 43 ARG cc_start: 0.8601 (mtm110) cc_final: 0.8224 (ttt180) REVERT: U 55 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.7998 (tpp80) REVERT: U 59 ASP cc_start: 0.8988 (m-30) cc_final: 0.8497 (m-30) REVERT: U 80 ASN cc_start: 0.9250 (t0) cc_final: 0.8985 (t0) outliers start: 29 outliers final: 22 residues processed: 338 average time/residue: 0.1948 time to fit residues: 106.2419 Evaluate side-chains 336 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 309 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 0.9990 chunk 354 optimal weight: 3.9990 chunk 387 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 370 optimal weight: 4.9990 chunk 229 optimal weight: 0.0020 chunk 209 optimal weight: 2.9990 chunk 377 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN D 90 HIS M 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.068716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.053444 restraints weight = 75116.800| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.41 r_work: 0.2555 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.320 33382 Z= 0.099 Angle : 0.501 12.504 45365 Z= 0.239 Chirality : 0.039 0.139 4962 Planarity : 0.003 0.050 5700 Dihedral : 8.524 88.374 4822 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.75 % Allowed : 12.81 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.14), residues: 3955 helix: 2.32 (0.11), residues: 2172 sheet: 0.93 (0.27), residues: 369 loop : 0.87 (0.18), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 144 TYR 0.021 0.001 TYR O 309 PHE 0.013 0.001 PHE N 164 TRP 0.011 0.001 TRP C 142 HIS 0.014 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (33367) covalent geometry : angle 0.49818 / 0.24 (45352) SS BOND : bond 0.00197 / 0.12 ( 5) SS BOND : angle 0.92781 / 0.45 ( 10) hydrogen bonds : bond 0.03387 / 2.21 ( 1889) hydrogen bonds : angle 4.08208 / 2.90 ( 5334) metal coordination : bond 0.00570 / 0.28 ( 4) metal coordination : angle 6.01952 / 3.26 ( 3) Misc. bond : bond 0.22159 / 12.57 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6634.53 seconds wall clock time: 114 minutes 43.64 seconds (6883.64 seconds total)